FastPop is an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins.
Multilocus has been written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, various linkage disequilibrium indices, and a measure of population differentiation, and allows one to search for subpopulations which do not share polymorphisms (and thus might be reproductively isolated). It includes a modification of the IA (Index of Association) metric that corrects the scaling effect seen when one applies the metric to different numbers of loci. In addition, there are randomization routines which allow one to test various null hypotheses.
Paul-Michael Agapow and Austin Burt (firstname.lastname@example.org), Dept. Biology, University College London
PERMUT computes measures of diversity and differenciation from haploid population genetic data, when a measure of the distance between haplotypes is available,and test whether the differentiation and diversity measures differ from the equivalent measures that do not take into account the distances between haplotypes
CpSSR computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered
Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux
QDB (Quick DataBase) is a general database program suitable for managing genetic data which runs under Windows. QDB essentially consists of form-based facilities to edit data and facilities to generate reports using its own (idiosyncratic) language. There is provision to import and export data to and from text files and other DBF files. QDB basically works as a flat file database, but there is a facility for relational look- ups into other DBF files which can be used to obtain data in reports and in automatically calculated fields. Some aspects of QDB are modelled on Buttonware’s PC-File and in some areas there is near-compatibility between the programs.